app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java

   1 /**
   2  * Copyright (C) 2007 EDIT
   3  * European Distributed Institute of Taxonomy
   4  * http://www.e-taxonomy.eu
   5  *
   6  * The contents of this file are subject to the Mozilla Public License Version 1.1
   7  * See LICENSE.TXT at the top of this package for the full license terms.
   8  */
   9
  10 package eu.etaxonomy.cdm.io.redlist.gefaesspflanzen;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.common.CdmUtils;
  24 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  25 import eu.etaxonomy.cdm.io.common.DbImportBase;
  26 import eu.etaxonomy.cdm.io.common.IPartitionedIO;
  27 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  28 import eu.etaxonomy.cdm.model.common.CdmBase;
  29 import eu.etaxonomy.cdm.model.common.Language;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  32 import eu.etaxonomy.cdm.model.taxon.Classification;
  33 import eu.etaxonomy.cdm.model.taxon.Synonym;
  34 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  35 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  36 import eu.etaxonomy.cdm.model.taxon.Taxon;
  37 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  38
  39 /**
  40  *
  41  * @author pplitzner
  42  * @date Mar 1, 2016
  43  *
  44  */
  45
  46 @Component
  47 @SuppressWarnings("serial")
  48 public class RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  49
  50     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportClassification.class);
  51
  52     private static final String tableName = "Rote Liste Gefäßpflanzen";
  53
  54     private static final String pluralString = "classifications";
  55
  56     public RedListGefaesspflanzenImportClassification() {
  57         super(tableName, pluralString);
  58     }
  59
  60     @Override
  61     protected String getIdQuery(RedListGefaesspflanzenImportState state) {
  62         return "SELECT NAMNR "
  63                 + "FROM V_TAXATLAS_D20_EXPORT t "
  64                 + " ORDER BY NAMNR";
  65     }
  66
  67     @Override
  68     protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
  69         String result = " SELECT * "
  70                 + " FROM V_TAXATLAS_D20_EXPORT t "
  71                 + " WHERE t.NAMNR IN (@IDSET)";
  72         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  73         return result;
  74     }
  75
  76     @Override
  77     protected void doInvoke(RedListGefaesspflanzenImportState state) {
  78         makeClassification("Gesamtliste", state.getConfig().getClassificationUuid(), "Gesamtliste_ref", RedListUtil.gesamtListeReferenceUuid, state);
  79         makeClassification("Checkliste", RedListUtil.checkListClassificationUuid, "Checkliste_ref", RedListUtil.checkListReferenceUuid, state);
  80         makeClassification("E", RedListUtil.uuidClassificationE, "E_ref", RedListUtil.uuidClassificationReferenceE, state);
  81         makeClassification("W", RedListUtil.uuidClassificationW, "W_ref", RedListUtil.uuidClassificationReferenceW, state);
  82         makeClassification("K", RedListUtil.uuidClassificationK, "K_ref", RedListUtil.uuidClassificationReferenceK, state);
  83         makeClassification("AW", RedListUtil.uuidClassificationAW, "AW_ref", RedListUtil.uuidClassificationReferenceAW, state);
  84         makeClassification("AO", RedListUtil.uuidClassificationAO, "AO_ref", RedListUtil.uuidClassificationReferenceAO, state);
  85         makeClassification("R", RedListUtil.uuidClassificationR, "R_ref", RedListUtil.uuidClassificationReferenceR, state);
  86         makeClassification("O", RedListUtil.uuidClassificationO, "O_ref", RedListUtil.uuidClassificationReferenceO, state);
  87         makeClassification("S", RedListUtil.uuidClassificationS, "S_ref", RedListUtil.uuidClassificationReferenceS, state);
  88         super.doInvoke(state);
  89     }
  90
  91
  92     @Override
  93     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
  94         ResultSet rs = partitioner.getResultSet();
  95         Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid());
  96         Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid);
  97         Classification classificationE = getClassificationService().load(RedListUtil.uuidClassificationE);
  98         Classification classificationW = getClassificationService().load(RedListUtil.uuidClassificationW);
  99         Classification classificationK = getClassificationService().load(RedListUtil.uuidClassificationK);
 100         Classification classificationAW = getClassificationService().load(RedListUtil.uuidClassificationAW);
 101         Classification classificationAO = getClassificationService().load(RedListUtil.uuidClassificationAO);
 102         Classification classificationR = getClassificationService().load(RedListUtil.uuidClassificationR);
 103         Classification classificationO = getClassificationService().load(RedListUtil.uuidClassificationO);
 104         Classification classificationS = getClassificationService().load(RedListUtil.uuidClassificationS);
 105         try {
 106             while (rs.next()){
 107                 makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification,
 108                         classificationE, classificationW, classificationK, classificationAW
 109                         , classificationAO, classificationR, classificationO, classificationS);
 110
 111             }
 112         } catch (SQLException e) {
 113             e.printStackTrace();
 114         }
 115
 116         logger.info("Update classification (1000 nodes)");
 117         getClassificationService().saveOrUpdate(gesamtListeClassification);
 118         getClassificationService().saveOrUpdate(checklistClassification);
 119         return true;
 120     }
 121
 122     private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs,
 123             Classification gesamtListeClassification, Classification checklistClassification,
 124             Classification classificationE, Classification classificationW, Classification classificationK,
 125             Classification classificationAW, Classification classificationAO, Classification classificationR,
 126             Classification classificationO, Classification classificationS)
 127             throws SQLException {
 128         long id = rs.getLong(RedListUtil.NAMNR);
 129         String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));
 130         String gueltString = rs.getString(RedListUtil.GUELT);
 131         String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
 132
 133         //Gesamtliste
 134         TaxonBase taxonBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
 135         Taxon parentGL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);
 136         createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);
 137
 138         //Checkliste
 139         TaxonBase taxonBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
 140         Taxon parentCL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);
 141         if(taxonBaseCL!=null){//null check necessary because not all taxa exist in the checklist
 142             createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);
 143         }
 144
 145         if(taxonBaseGL!= null && taxonBaseCL!=null
 146                 && taxonBaseGL.getUuid().equals(taxonBaseCL.getUuid())){
 147             RedListUtil.logMessage(id, "Same UUID for "+taxonBaseGL+ " (Gesamtliste) and "+taxonBaseCL+" (Checkliste)", logger);
 148         }
 149         if(parentGL!=null && parentCL!=null && parentGL.getUuid().equals(parentCL.getUuid())){
 150             RedListUtil.logMessage(id, "Same UUID for "+parentGL+ " (Gesamtliste) and "+parentCL+" (Checkliste)", logger);
 151         }
 152
 153         //add taxa for concept relationships to E, W, K, AW, AO, R, O, S
 154         addTaxonToClassification(classificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, id, state);
 155         addTaxonToClassification(classificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, id, state);
 156         addTaxonToClassification(classificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, id, state);
 157         addTaxonToClassification(classificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, id, state);
 158         addTaxonToClassification(classificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, id, state);
 159         addTaxonToClassification(classificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, id, state);
 160         addTaxonToClassification(classificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, id, state);
 161         addTaxonToClassification(classificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, id, state);
 162     }
 163
 164     private void addTaxonToClassification(Classification classification, String classificationNamespace, long id, RedListGefaesspflanzenImportState state){
 165         Taxon taxon = HibernateProxyHelper.deproxy(state.getRelatedObject(classificationNamespace, String.valueOf(id), TaxonBase.class), Taxon.class);
 166         classification.addChildTaxon(taxon, null, null);
 167     }
 168
 169     private void createParentChildNodes(Classification classification, long id, String gueltString,
 170             String taxZusatzString, TaxonBase taxonBase, Taxon parent) {
 171         if(taxonBase==null){
 172             RedListUtil.logMessage(id, "child taxon/synonym of "+parent+"  is null. ("+classification.getTitleCache()+")" , logger);
 173             return;
 174         }
 175         //taxon
 176         if(taxonBase.isInstanceOf(Taxon.class)){
 177             //misapplied name
 178             String appendedPhrase = taxonBase.getAppendedPhrase();
 179             if(appendedPhrase!=null && appendedPhrase.equals(RedListUtil.AUCT)){
 180                 if(parent==null){
 181                     RedListUtil.logMessage(id, "parent taxon of misapplied name "+taxonBase+"  is null. ("+classification.getTitleCache()+")" , logger);
 182                     return;
 183                 }
 184                 parent.addMisappliedName((Taxon) taxonBase, null, null);
 185             }
 186             else{
 187                 classification.addParentChild(parent, (Taxon)taxonBase, null, null);
 188             }
 189
 190             if(CdmUtils.isNotBlank(taxZusatzString)){
 191                 if(taxZusatzString.trim().equals("p. p.")){
 192                     RedListUtil.logMessage(id, "pro parte for accepted taxon "+taxonBase, logger);
 193                 }
 194             }
 195         }
 196         //synonym
 197         else if(taxonBase.isInstanceOf(Synonym.class)){
 198             if(parent==null){
 199                 RedListUtil.logMessage(id, "parent taxon of synonym "+taxonBase+"  is null. ("+classification.getTitleCache()+")" , logger);
 200                 return;
 201             }
 202             //basionym
 203             if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){
 204                 parent.addHomotypicSynonym((Synonym) taxonBase, null, null);
 205                 parent.getName().addBasionym(taxonBase.getName());
 206             }
 207             //regular synonym
 208             else{
 209                 SynonymRelationship synonymRelationship = parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);
 210
 211                 //TAX_ZUSATZ
 212                 if(CdmUtils.isNotBlank(taxZusatzString)){
 213                     if(taxZusatzString.trim().equals("p. p.")){
 214                         synonymRelationship.setProParte(true);
 215                     }
 216                     else if(taxZusatzString.trim().equals("s. l. p. p.")){
 217                         synonymRelationship.setProParte(true);
 218                         taxonBase.setAppendedPhrase("s. l.");
 219                     }
 220                     else if(taxZusatzString.trim().equals("s. str. p. p.")){
 221                         synonymRelationship.setProParte(true);
 222                         taxonBase.setAppendedPhrase("s. str.");
 223                     }
 224                     else if(taxZusatzString.trim().equals("s. l.")
 225                             || taxZusatzString.trim().equals("s. str.")){
 226                         taxonBase.setAppendedPhrase(taxZusatzString);
 227                     }
 228                     else{
 229                         RedListUtil.logMessage(id, "unknown value "+taxZusatzString+" for column "+RedListUtil.TAX_ZUSATZ, logger);
 230                     }
 231                 }
 232             }
 233         }
 234         //set sec reference
 235         taxonBase.setSec(classification.getReference());
 236         taxonBase.setTitleCache(null, false);//refresh title cache
 237     }
 238
 239     @Override
 240     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 241             RedListGefaesspflanzenImportState state) {
 242         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 243
 244         Set<String> idSet = new HashSet<String>();
 245         try {
 246             while (rs.next()){
 247                 idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));
 248                 idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));
 249             }
 250         } catch (SQLException e) {
 251             e.printStackTrace();
 252         }
 253         Map<String, TaxonBase> taxonMapGesamtListe = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
 254         result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, taxonMapGesamtListe);
 255         Map<String, TaxonBase> taxonMapCheckliste = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
 256         result.put(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, taxonMapCheckliste);
 257         return result;
 258     }
 259
 260     private void makeClassification(String classificationName, UUID classificationUuid, String referenceName, UUID referenceUuid, RedListGefaesspflanzenImportState state) {
 261         Classification classification = Classification.NewInstance(classificationName, Language.DEFAULT());
 262         classification.setUuid(classificationUuid);
 263         Reference gesamtListeReference = ReferenceFactory.newGeneric();
 264         gesamtListeReference.setTitle(referenceName);
 265         gesamtListeReference.setUuid(referenceUuid);
 266         classification.setReference(gesamtListeReference);
 267         getClassificationService().save(classification);
 268     }
 269
 270     @Override
 271     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 272         return false;
 273     }
 274
 275     @Override
 276     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 277         return false;
 278     }
 279
 280 }